- * The following steps came from Effective Java Programming - * Language Guide by Joshua Bloch, Chapter 3 - * - * @return a hash code value for the object. - */ - public int hashCode( - ) { - int result = super.hashCode(); - - long tmp; - if (_seqRef != null) { - result = 37 * result + _seqRef.hashCode(); - } - if (_provenance != null) { - result = 37 * result + _provenance.hashCode(); - } - - return result; - } + return _seqRef.get(index); + } - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid( - ) { - try { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } + /** + * Method getSeqRef.Returns the contents of the collection in an Array. + *
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public java.lang.Object[] getSeqRef() { + java.lang.Object[] array = new java.lang.Object[0]; + return (java.lang.Object[]) this._seqRef.toArray(array); + } - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void marshal( - final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, out); - } + /** + * Method getSeqRefAsReference.Returns a reference to '_seqRef'. No type + * checking is performed on any modifications to the Vector. + * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getSeqRefAsReference() { + return this._seqRef; + } - /** - * - * - * @param handler - * @throws java.io.IOException if an IOException occurs during - * marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - */ - public void marshal( - final org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - Marshaller.marshal(this, handler); - } + /** + * Method getSeqRefCount. + * + * @return the size of this collection + */ + public int getSeqRefCount() { + return this._seqRef.size(); + } - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance( - final uk.ac.vamsas.objects.core.Provenance provenance) { - this._provenance = provenance; + /** + * Overrides the java.lang.Object.hashCode method. + *
+ * The following steps came from Effective Java Programming Language + * Guide by Joshua Bloch, Chapter 3 + * + * @return a hash code value for the object. + */ + public int hashCode() { + int result = super.hashCode(); + + long tmp; + if (_seqRef != null + && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) { + result = 37 * result + _seqRef.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef); + } + if (_provenance != null + && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + result = 37 * result + _provenance.hashCode(); + org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); } - /** - * Sets the value of field 'seqRef'. The field 'seqRef' has the - * following description: annotation is associated with a - * particular dataset sequence - * - * @param seqRef the value of field 'seqRef'. - */ - public void setSeqRef( - final java.lang.Object seqRef) { - this._seqRef = seqRef; + return result; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid() { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + */ + public void marshal(final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException if object is - * null or if any SAXException is thrown during marshaling - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType + /** + * + * + * @param handler + * @throws java.io.IOException + * if an IOException occurs during marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + */ + public void marshal(final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** */ - public static uk.ac.vamsas.objects.core.RangeType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSetAnnotations.class, reader); + public void removeAllSeqRef() { + this._seqRef.clear(); + } + + /** + * Method removeSeqRef. + * + * @param vSeqRef + * @return true if the object was removed from the collection. + */ + public boolean removeSeqRef(final java.lang.Object vSeqRef) { + boolean removed = _seqRef.remove(vSeqRef); + return removed; + } + + /** + * Method removeSeqRefAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.Object removeSeqRefAt(final int index) { + java.lang.Object obj = this._seqRef.remove(index); + return obj; + } + + /** + * Sets the value of field 'provenance'. + * + * @param provenance + * the value of field 'provenance'. + */ + public void setProvenance( + final uk.ac.vamsas.objects.core.Provenance provenance) { + this._provenance = provenance; + } + + /** + * + * + * @param index + * @param vSeqRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setSeqRef(final int index, final java.lang.Object vSeqRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqRef.size()) { + throw new IndexOutOfBoundsException("setSeqRef: Index value '" + index + + "' not in range [0.." + (this._seqRef.size() - 1) + "]"); } - /** - * - * - * @throws org.exolab.castor.xml.ValidationException if this - * object is an invalid instance according to the schema - */ - public void validate( - ) - throws org.exolab.castor.xml.ValidationException { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); + this._seqRef.set(index, vSeqRef); + } + + /** + * + * + * @param vSeqRefArray + */ + public void setSeqRef(final java.lang.Object[] vSeqRefArray) { + // -- copy array + _seqRef.clear(); + + for (int i = 0; i < vSeqRefArray.length; i++) { + this._seqRef.add(vSeqRefArray[i]); } + } + + /** + * Sets the value of '_seqRef' by copying the given Vector. All elements will + * be checked for type safety. + * + * @param vSeqRefList + * the Vector to copy. + */ + public void setSeqRef(final java.util.Vector vSeqRefList) { + // copy vector + this._seqRef.clear(); + + this._seqRef.addAll(vSeqRefList); + } + + /** + * Sets the value of '_seqRef' by setting it to the given Vector. No type + * checking is performed. + * + * @deprecated + * + * @param seqRefVector + * the Vector to set. + */ + public void setSeqRefAsReference(final java.util.Vector seqRefVector) { + this._seqRef = seqRefVector; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException + * if object is null or if any SAXException is thrown during + * marshaling + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType + */ + public static uk.ac.vamsas.objects.core.RangeType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal( + uk.ac.vamsas.objects.core.DataSetAnnotations.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + */ + public void validate() throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } }